There are advantages in the arrangement ahend describes, but I wound up going for a single 36V pack and a single charger.
There is an outfit down there in the U.S. (I'm in Canada) that sells a single solution charger that works very well.
http://www.powerstream.com/nimh-3pn9-36V.htmThe unit uses all three methods of determining end-of-charge (voltage, temperature, and time - if all else fails), but in order to make it sing, you have to include a thermistor in your pack when you're building it (no big deal). If making sense of the thermistor specification leaves you cold, I can tell you the Digikey part number for a devices which meets spec (and is what I am using) is 317-1309-ND. They're only around $2.00 each, and only need to be taped to the outside of one of the cells in the middle of the pack to be completely effective.
The charger also has the ability to automatically DISCHARGE the 36V pack down to 1V per cell and commence a re-charge, should you feel a need to cycle the pack without running it down naturally.
So far, so good on this end, and the price is less than 3 discrete 12V chargers while at the same time reducing the amount of "plumbing" required to hook everything up. The units ship with a 3 prong "microphone" style plug (which I lopped off and replaced with something that suits my pack), and they provide the wiring diagram with the charger. Just note that the diagram they show you is looking into the end of the expected receptacle - NOT the end of the plug on the charger. If you cut the wire, brown is charge+, blue is ground, and green/yellow is the thermistor. The thermistor simply installs between the green/yellow and ground with no extra components.
The other thing of important note about this charger is that it seems to use a pulse method to charge, rather than a constant current. Arguably, this much better for NiMh batteries (I wish I could find a definitive technical document to support/refute this), as it takes voltage readings between pulses - the dip in pack voltage upon end-of-charge is harder to detect on NiMh cells than NiCd, and measuring when the charger isn't supplying its own bias makes this easier. The other claim is that pulsing is beneficial to maintaining the chemistry of nickel-based batteries. Can't comment. All I know is it works great :-)
Cheers!